REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0084AL017_2 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : SJOLANDER-THOMAS 
REMARK  ---------------------------------------------------------- 
TARGET T0084  
AUTHOR 5827-4749-3439  
METHOD HMM alignment for T0084   
METHOD  
METHOD As usual, we employed a two-pronged approach: (1) We scored the target   
METHOD against all the HMMs and threading models in our libraries, and (2) we   
METHOD gathered homologs to the target using one or more tools  
METHOD (such as iterated FASTA or PsiBLAST), constructed an   
METHOD HMM for the target and homologs (using UCSC's HMM software), and   
METHOD scored PDB. This yielded three sets of scores, which we then used   
METHOD to find a target-structure match.  
METHOD   
METHOD Not surprisingly, given that the target is an artificial  
METHOD construct, BLAST produced no homologs to the target.   
METHOD However, when we scored all the HMMs in our library,  
METHOD one structure had a weak but significant score: d2ztaa.  
METHOD When we examined the alignment of the target and   
METHOD structure we discovered the two sequences were perfect  
METHOD reversals of each other.   
METHOD The HMM alignment in this submission shows several  
METHOD identities. Normally, we would have more confidence  
METHOD in an alignment that maximized identities between  
METHOD two proteins that are related by evolution.  
METHOD Since, however, these two proteins are not thus related,  
METHOD we decided to make the threading alignment model 1,  
METHOD and the HMM alignment model 2, under the presumption  
METHOD that the threading alignment may be closer to   
METHOD a physically plausible structure.  
METHOD   
METHOD This alignment was generated by aligning the target  
METHOD and structure to an HMM trained on the structure  
METHOD and its close homologs. As usual, the alignment  
METHOD has not been edited in any way from the automatic   
METHOD alignment produced.  
METHOD  
MODEL 2  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 2zta_A 
ATOM      1  N   CYS     1      37.494  13.382  15.829  1.00  0.00              
ATOM      2  CA  CYS     1      38.127  14.684  15.695  1.00  0.00              
ATOM      3  C   CYS     1      37.179  15.790  15.306  1.00  0.00              
ATOM      4  O   CYS     1      36.239  15.576  14.555  1.00  0.00              
ATOM      5  N   GLY     2      37.447  16.947  15.901  1.00  0.00              
ATOM      6  CA  GLY     2      36.661  18.155  15.840  1.00  0.00              
ATOM      7  C   GLY     2      36.279  18.671  14.490  1.00  0.00              
ATOM      8  O   GLY     2      35.112  19.078  14.259  1.00  0.00              
ATOM      9  N   GLY     3      37.334  18.677  13.666  1.00  0.00              
ATOM     10  CA  GLY     3      37.330  19.059  12.267  1.00  0.00              
ATOM     11  C   GLY     3      36.361  18.171  11.532  1.00  0.00              
ATOM     12  O   GLY     3      35.348  18.645  11.036  1.00  0.00              
ATOM     13  N   ARG     4      36.630  16.866  11.489  1.00  0.00              
ATOM     14  CA  ARG     4      35.671  15.982  10.839  1.00  0.00              
ATOM     15  C   ARG     4      34.203  16.207  11.309  1.00  0.00              
ATOM     16  O   ARG     4      33.250  16.103  10.533  1.00  0.00              
ATOM     17  N   GLU     5      28.239  20.961   8.817  1.00  0.00              
ATOM     18  CA  GLU     5      28.153  21.876   7.674  1.00  0.00              
ATOM     19  C   GLU     5      27.513  21.208   6.465  1.00  0.00              
ATOM     20  O   GLU     5      26.657  21.739   5.763  1.00  0.00              
ATOM     21  N   GLY     6      27.889  19.970   6.297  1.00  0.00              
ATOM     22  CA  GLY     6      27.355  19.150   5.237  1.00  0.00              
ATOM     23  C   GLY     6      25.921  18.827   5.431  1.00  0.00              
ATOM     24  O   GLY     6      25.231  18.837   4.430  1.00  0.00              
ATOM     25  N   VAL     7      25.516  18.443   6.673  1.00  0.00              
ATOM     26  CA  VAL     7      24.139  18.084   6.963  1.00  0.00              
ATOM     27  C   VAL     7      23.279  19.279   6.875  1.00  0.00              
ATOM     28  O   VAL     7      22.186  19.189   6.384  1.00  0.00              
ATOM     29  N   LEU     8      23.765  20.415   7.323  1.00  0.00              
ATOM     30  CA  LEU     8      22.953  21.628   7.228  1.00  0.00              
ATOM     31  C   LEU     8      22.604  22.010   5.740  1.00  0.00              
ATOM     32  O   LEU     8      21.470  22.358   5.332  1.00  0.00              
ATOM     33  N   LYS     9      23.646  21.917   4.934  1.00  0.00              
ATOM     34  CA  LYS     9      23.635  22.121   3.513  1.00  0.00              
ATOM     35  C   LYS     9      22.646  21.127   2.832  1.00  0.00              
ATOM     36  O   LYS     9      21.785  21.529   2.057  1.00  0.00              
ATOM     37  N   LYS    10      22.683  19.813   3.160  1.00  0.00              
ATOM     38  CA  LYS    10      21.673  18.905   2.595  1.00  0.00              
ATOM     39  C   LYS    10      20.294  19.295   3.079  1.00  0.00              
ATOM     40  O   LYS    10      19.328  19.265   2.308  1.00  0.00              
ATOM     41  N   LEU    11      20.197  19.618   4.379  1.00  0.00              
ATOM     42  CA  LEU    11      18.920  20.029   4.916  1.00  0.00              
ATOM     43  C   LEU    11      18.309  21.239   4.222  1.00  0.00              
ATOM     44  O   LEU    11      17.156  21.194   3.870  1.00  0.00              
ATOM     45  N   ARG    12      19.061  22.299   4.002  1.00  0.00              
ATOM     46  CA  ARG    12      18.583  23.458   3.271  1.00  0.00              
ATOM     47  C   ARG    12      18.128  23.043   1.844  1.00  0.00              
ATOM     48  O   ARG    12      17.125  23.509   1.347  1.00  0.00              
ATOM     49  N   ALA    13      18.860  22.130   1.184  1.00  0.00              
ATOM     50  CA  ALA    13      18.464  21.654  -0.143  1.00  0.00              
ATOM     51  C   ALA    13      17.085  21.019  -0.057  1.00  0.00              
ATOM     52  O   ALA    13      16.234  21.259  -0.906  1.00  0.00              
ATOM     53  N   VAL    14      16.864  20.173   0.967  1.00  0.00              
ATOM     54  CA  VAL    14      15.562  19.515   1.148  1.00  0.00              
ATOM     55  C   VAL    14      14.448  20.469   1.537  1.00  0.00              
ATOM     56  O   VAL    14      13.294  20.298   1.171  1.00  0.00              
ATOM     57  N   GLU    15      14.762  21.483   2.300  1.00  0.00              
ATOM     58  CA  GLU    15      13.734  22.442   2.621  1.00  0.00              
ATOM     59  C   GLU    15      13.382  23.262   1.357  1.00  0.00              
ATOM     60  O   GLU    15      12.257  23.689   1.201  1.00  0.00              
ATOM     61  N   ASN    16      14.350  23.531   0.462  1.00  0.00              
ATOM     62  CA  ASN    16      14.082  24.250  -0.792  1.00  0.00              
ATOM     63  C   ASN    16      13.093  23.412  -1.614  1.00  0.00              
ATOM     64  O   ASN    16      12.058  23.904  -2.029  1.00  0.00              
ATOM     65  N   GLU    17      13.371  22.115  -1.777  1.00  0.00              
ATOM     66  CA  GLU    17      12.464  21.235  -2.495  1.00  0.00              
ATOM     67  C   GLU    17      11.028  21.230  -1.953  1.00  0.00              
ATOM     68  O   GLU    17      10.067  21.224  -2.727  1.00  0.00              
ATOM     69  N   LEU    18      10.885  21.144  -0.615  1.00  0.00              
ATOM     70  CA  LEU    18       9.567  21.098   0.055  1.00  0.00              
ATOM     71  C   LEU    18       8.693  22.337  -0.258  1.00  0.00              
ATOM     72  O   LEU    18       7.471  22.279  -0.331  1.00  0.00              
ATOM     73  N   HIS    19       9.339  23.476  -0.392  1.00  0.00              
ATOM     74  CA  HIS    19       8.696  24.740  -0.647  1.00  0.00              
ATOM     75  C   HIS    19       8.274  24.857  -2.089  1.00  0.00              
ATOM     76  O   HIS    19       7.348  25.560  -2.458  1.00  0.00              
ATOM     77  N   TYR    20       9.023  24.199  -2.915  1.00  0.00              
ATOM     78  CA  TYR    20       8.757  24.218  -4.310  1.00  0.00              
ATOM     79  C   TYR    20       7.617  23.282  -4.527  1.00  0.00              
ATOM     80  O   TYR    20       6.727  23.570  -5.329  1.00  0.00              
ATOM     81  N   ASN    21       7.652  22.156  -3.780  1.00  0.00              
ATOM     82  CA  ASN    21       6.581  21.183  -3.911  1.00  0.00              
ATOM     83  C   ASN    21       5.314  21.638  -3.285  1.00  0.00              
ATOM     84  O   ASN    21       4.262  21.231  -3.717  1.00  0.00              
ATOM     85  N   LYS    22       5.442  22.526  -2.316  1.00  0.00              
ATOM     86  CA  LYS    22       4.334  23.132  -1.617  1.00  0.00              
ATOM     87  C   LYS    22       3.522  24.052  -2.531  1.00  0.00              
ATOM     88  O   LYS    22       2.278  24.009  -2.547  1.00  0.00              
ATOM     89  N   SER    23       4.293  24.835  -3.302  1.00  0.00              
ATOM     90  CA  SER    23       3.872  25.752  -4.340  1.00  0.00              
ATOM     91  C   SER    23       3.127  24.938  -5.434  1.00  0.00              
ATOM     92  O   SER    23       2.077  25.324  -5.942  1.00  0.00              
ATOM     93  N   LEU    24       3.617  23.731  -5.731  1.00  0.00              
ATOM     94  CA  LEU    24       2.917  22.842  -6.655  1.00  0.00              
ATOM     95  C   LEU    24       1.523  22.471  -6.133  1.00  0.00              
ATOM     96  O   LEU    24       0.595  22.391  -6.906  1.00  0.00              
ATOM     97  N   LEU    25       1.411  22.161  -4.828  1.00  0.00              
ATOM     98  CA  LEU    25       0.184  21.709  -4.154  1.00  0.00              
ATOM     99  C   LEU    25      -0.970  22.690  -4.228  1.00  0.00              
ATOM    100  O   LEU    25      -2.127  22.345  -4.499  1.00  0.00              
END
